Even without a triple axel, I think Alysa will make the US Olympic team. In this transition year, Alysa still did solid triple-triples (which can't be said for most of the US ladies), and she was also the only one to put them in the second half of her short program (and in the free, it was only her and Bradie that backloaded 3+3s). As others have mentioned, she has a great competitive mentality. Alysa doesn't let falls get to her, and she rarely pops, which is especially helpful for scores since a fall on a rotated triple jump is worth far more than a popped triple. The only pop I can remember her doing is the 2F in the Nationals free program this year (I'm not counting the Las Vegas Invitational, since all those doubles were intentional). Further, while Alysa is prone to carrots, the rest of the US ladies are just as, if not, more prone to underrotations. Without the 3A, Alysa still has a BV advantage on most of the US ladies as a result. Plus, she put in serious work in her components and significantly cut down the PCS gap between herself and the other top US ladies. Last year, Alysa had a 68 in PCS in the free program, while Mariah scored a 75 and Bradie scored a 71. This year, Alysa had 70 in PCS while the highest PCS went to Bradie, who had a 74. That seven point gap went to a four point gap and it shrank more in the short program. This year, Alysa had a 35 while Bradie had a 37. Last year, Alysa had a 32 while Bradie had a 36. Four point gap went to two point gap. Overall, Alysa cut the PCS difference from eleven points to six points, nearly halving it. Thus, she's not nearly as reliant on her ultra-C jumps anymore, and deservedly so. Alysa clearly put a lot of work into improving her components, and I'm glad that it's reflecting in the scores.
Whether Alysa can have a podium chance will depend on the ultra-C elements. With just a consistent triple axel, she would probably slot into the top 5 and have an outside hope of the podium if one of the three Russians or Rika makes mistake. I say this because with a triple axel, she has a significant BV advantage over all the other ladies besides the Russians, Rika, Young You, and Wakaba Higuchi. A 3A in particular is far more valuable than any quad since it can be used in the short program to make a significant BV difference. This BV advantage makes up for the slight PCS disadvantage she would have. Then among the elite group of ladies who have an ultra-C element, I think Alysa would score higher in PCS than Young You. As for Wakaba, I feel like JFed has been trying to drop her hard, and I don't see her making the Japanese Olympic team.